A base gemstone is considered uncut, or rough. When it is a cut the value of it increases dramatically by 50%.
A cut and polished gemstone is made for jewelry. The labor, expertise and equipment that are used to cut and polish or to facet a stone become part of the cost of that stone.
It takes several hours to cut a gram of rough sapphire into a 1ct gemstone. Unless the facets are very precise, and the proportions are good, the finished piece will not have great value. It takes enormous skill and a very good eye to facet gemstones. That expertise comes at a price.
Typically gnomes, and dwarves have excellent tools and eyesight and a feeling for stone which make them excellent jewelers.
Cutting a stone can be done with jewelers tools. For the sake of the game, no weight of the stone is lost, but there is a risk when cutting the stone. The DC is 10 with slight of hand or perception and requires Jewelery Tools and requires Na with them.
If the check is failed the rough (or original stone) is DESTROYED. This is why only the best jewelers are allowed to work with the stone preventing the value of the stone to be lost.